Pursuant to Section 13 or 15(d) of the Securities
Exchange Act of 1934

Date of report (date of earliest event reported):
November 14, 2019

TONIX PHARMACEUTICALS HOLDING CORP.

(Exact
name of registrant as specified in its charter)

Nevada

001-36019

26-1434750

(State
or Other Jurisdiction

of
Incorporation)

(Commission

File
Number)

(IRS
Employer

Identification
No.)

509
Madison Avenue, Suite 1608, New York, New York 10022

(Address
of principal executive offices) (Zip Code)

Registrant’s
telephone number, including area code: (212) 980-9155

Check
the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant
under any of the following provisions (see General Instruction A.2. below):

Indicate
by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§
230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§ 240.12b-2 of this chapter).

Emerging
growth company ☐

If
an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for
complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.
☐

Item
1.01. Entry into a Material Definitive Agreement.

On
November 14, 2019, Tonix Pharmaceuticals Holding Corp., a Nevada corporation (the “Company”), entered into an underwriting
agreement (the “Underwriting Agreement”) with A.G.P./Alliance Global Partners (the “Underwriter”), pursuant
to which the Company agreed to issue and sell to the Underwriter in a firm commitment underwritten public offering (the “Offering”)
an aggregate of (i) 547,420 Class A Units (the “Class A Units”), with each Class A Unit consisting of one share of
the Company’s common stock, par value $0.001 per share (the “Common Stock”), one five-year warrant (each, a
“Warrant” and collectively, the “Warrants”) to purchase one share of Common Stock at an exercise price
equal to $1.94 per share of Common Stock, and one one-year common warrant to purchase one-half of a share of Common Stock at an
exercise price equal to $1.94 per share of Common Stock (each, a “Common Warrant”, and collectively, the “Common
Warrants”), with each Class A Unit to be offered to the public at a public offering price of $1.94, and (ii) 7,938 Class
B Units (the “Class B Units”, and together with the Class A Units, the “Units”), with each Class B Unit
offered to the public at a public offering price of $1,000 per Class B Unit and consisting of one share of the Company’s
Series A Convertible Preferred Stock (the “Series A Preferred Stock”), with a stated value of $1,000 and convertible
into 515.464 shares of Common Stock at the conversion price of $1.94 per share, one Warrant to purchase 515.464 shares of Common
Stock at an exercise price equal to $1.94 per share of Common Stock, and one Common Warrant to purchase 257.732 shares of Common
Stock at an exercise price equal to $1.94 per share of Common Stock. The Series A Preferred Stock will be convertible into an
aggregate of 4,091,752 shares of Common Stock, and issued with Warrants to purchase an aggregate of 4,091,752 shares of Common
Stock and Common Warrants to purchase an aggregate of 2,045,876 shares of Common Stock. The Offering is expected to close on November
19, 2019, subject to customary closing conditions.

The
Units are offered by the Company pursuant to a registration statement on Form S-1 (File No. 333-234263), as amended,
filed with the Securities and Exchange Commission (the “Commission”), which was declared effective by the Commission
on November 14, 2019 (the “Registration Statement”).

The
conversion price of the Series A Preferred Stock and exercise price of the Warrants and Common Warrants are subject to appropriate
adjustment in the event of recapitalization events, stock dividends, stock splits, stock combinations, reclassifications, reorganizations
or similar events affecting the Company’s Common Stock.

The Warrants will be immediately
exercisable at a price of $1.94 per share of Common Stock (which is 100% of the public offering price of the Class A Units) and
will expire on November 13, 2024. The Warrants contain provisions for redemption at the Black-Scholes value upon certain fundamental
transactions. If at the time of exercise, there is no effective registration statement registering, or no current prospectus available
for, the issuance of the shares of Common Stock to the holder, then the Warrants may only be exercised through a cashless exercise.
No fractional shares of Common Stock will be issued in connection with the exercise of a Warrant. In lieu of fractional shares,
the holder will receive an amount in cash equal to the fractional amount multiplied by the fair market value of any such fractional
shares.

The
Common Warrants will be immediately exercisable at a price of $1.94 per share of Common Stock (which is 100% of the public offering
price of the Class A Units) and will expire on November 13, 2020. If at the time of exercise, there is no effective registration
statement registering, or no current prospectus available for, the issuance of the shares of Common Stock to the holder, then
the Warrants may only be exercised through a cashless exercise. In addition, during the period of time between (i) the date that
is the earlier of 30 days after issuance and the date by which an aggregate of $9.0 million of securities of the Company are traded
and (ii) the date that is 12 months after issuance, the Common Warrants may be exercised, at the option of the holder, through
a cashless exercise. No fractional shares of Common Stock will be issued in connection with the exercise of a Common Warrant.
In lieu of fractional shares, the holder will receive an amount in cash equal to the fractional amount multiplied by the fair
market value of any such fractional shares.

A
holder will not be entitled to exercise any Warrant or Common Warrant or convert any shares of the Series A Preferred Stock if,
upon giving effect to such exercise or conversion, it would cause the aggregate number of shares of Common Stock beneficially
owned by the holder (together with its affiliates) to exceed 4.99% of the number of shares of Common Stock outstanding immediately
after giving effect to the exercise. However, any holder may increase or decrease such percentage to any other percentage not
in excess of 9.99% upon at least 61 days’ prior notice from the holder to the Company.

The
net proceeds to the Company from the Offering, after deducting the Underwriters’ discounts, fees and expenses and the Company’s
estimated Offering expenses, and excluding the proceeds, if any, from the exercise of the Warrants issued in the Offering, are
expected to be approximately $8.1 million. The Company anticipates using the net proceeds from the Offering to fund Phase
3 development for our lead product candidate, TNX-102 SL, to advance the development of our other product candidates, including
in-licensed product candidates, to repurchase shares of our common stock pursuant to a stock buyback program, and for working
capital and other general corporate purposes.

The
Underwriting Agreement contains representations and warranties that the parties made to, and solely for the benefit of, the other
in the context of all of the terms and conditions of that agreement and in the context of the specific relationship between the
parties. The provisions of the Underwriting Agreement, including the representations and warranties contained therein, are
not for the benefit of any party other than the parties to such agreements and are not intended as documents for investors and
the public to obtain factual information about the current state of affairs of the parties to those documents and agreements.
Rather, investors and the public should look to other disclosures contained in the Company’s filings with the Securities
and Exchange Commission.

The
Company also entered into warrant agency agreements with its transfer agent, vStock Transfer, LLC, who will act as warrant agent
for the Company, setting forth the terms and conditions of the Warrants (the “Warrant Agency Agreement”) and Common
Warrants (the “Warrant Agreement”) sold in the Offering.

The
foregoing summaries of the terms of the Underwriting Agreement, the Warrant Agency Agreement and the Warrant Agreement are subject
to, and qualified in their entirety by reference to, the Underwriting Agreement, the Warrant Agency Agreement and the Warrant
Agreement, which are filed as Exhibits 1.01, 4.04 and 4.05, respectively, to the Registration Statement and are incorporated herein
by reference. The foregoing summaries of the terms of the Warrants and Common Warrants are subject to, and qualified in their
entirety by reference to, the Warrant and Common Warrant, which are filed as Exhibits 4.01 and 4.02 to this Current Report on
Form 8-K and are incorporated herein by reference.

Item
5.03. Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year.

In
connection with the Offering, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of the Series
A Preferred Stock (the “Certificate of Designation”) on November 14, 2019, with the Secretary of State of the State
of Nevada that became effective on November 14, 2019. The Certificate of Designation provides for the issuance of the shares of
Series A Preferred Stock. With certain exceptions, the shares of Series A Preferred Stock rank on par with the shares of the Common
Stock, in each case, as to dividend rights and distributions of assets upon liquidation, dissolution or winding up of the Company.

With
certain exceptions, as described in the Certificate of Designation, the shares of Series A Preferred Stock have no voting rights.
However, as long as any shares of Series A Preferred Stock remain outstanding, the Certificate of Designation provides that the
Company shall not, without the affirmative vote of holders of a majority of the then outstanding shares of Series A Preferred
Stock, (i) alter or change adversely the powers, preferences or rights given to the Series A Preferred Stock or alter or
amend the Certificate of Designation, (ii) amend the Company’s articles of incorporation or other charter documents
in any manner that adversely affects any rights of the holders, (iii) increase the number of authorized shares of Series
A Preferred Stock, or (iv) enter into any agreement with respect to any of the foregoing.

Each
share of Series A Preferred Stock is convertible at any time at the holder’s option into a number of shares of Common Stock
(subject to adjustment for reverse and forward stock splits, stock dividends, stock combinations and other similar transactions
as specified in the Certificate of Designation) at a conversion price equal to the stated value of the Series A Preferred Stock
of $1,000 divided by the public offering price of the Class A Units in the Offering, or 1.94.

Shares
of the Series A Preferred Stock are not entitled to receive any dividends, unless and until specifically declared by the Company’s
board of directors. The holders of the Series A Preferred Stock will participate, on an as-if-converted-to-common stock basis,
in any dividends to the holders of Common Stock. The Company is not obligated to redeem or repurchase any shares of Series A Preferred
Stock. Shares of Series A Preferred Stock are not otherwise entitled to any redemption rights or mandatory sinking fund or analogous
fund provisions.

The
terms of the Series A Preferred Stock are set forth in the Certificate of Designation, are not complete and are qualified in their
entirety by reference to the full text which is filed as Exhibit 3.01 hereto and incorporated by reference herein.

Item
8.01. Other Events.

On
November 15, 2019, the Company issued a press release announcing the pricing of the Offering. A copy of the press release is attached
hereto as Exhibit 99.01 and is incorporated herein by reference.

Forward-
Looking Statements

This
Current Report on Form 8-K contains certain forward-looking statements within the meaning of Section 27A of the Securities Act
of 1933 and Section 21E of the Securities Exchange Act of 1934 and Private Securities Litigation Reform Act, as amended, including
those relating to the consummation of the Offering, the Company’s product development, clinical trials, clinical and regulatory
timelines, market opportunity, competitive position, possible or assumed future results of operations, business strategies, potential
growth opportunities and other statement that are predictive in nature. These forward-looking statements are based on current
expectations, estimates, forecasts and projections about the industry and markets in which we operate and management’s current
beliefs and assumptions.

These
statements may be identified by the use of forward-looking expressions, including, but not limited to, “expect,” “anticipate,”
“intend,” “plan,” “believe,” “estimate,” “potential,” “predict,”
“project,” “should,” “would” and similar expressions and the negatives of those terms. These
statements relate to future events or our financial performance and involve known and unknown risks, uncertainties, and other
factors which may cause actual results, performance or achievements to be materially different from any future results, performance
or achievements expressed or implied by the forward-looking statements. Such factors include those set forth in the Company’s
filings with the Securities and Exchange Commission. Prospective investors are cautioned not to place undue reliance on such forward-looking
statements, which speak only as of the date of this press release. The Company undertakes no obligation to publicly update any
forward-looking statement, whether as a result of new information, future events or otherwise.